An OODB with entity-based persistence

An object-oriented database (P/FDM) has been built as a natural extension of Shipman's functional data model (FDM) which is itself founded on entity-relationship concepts. The authors are using this (P.H.D. Gray et al., 1990), to store 50 Mb of protein structure data, including the coordinates of every atom in over 80 proteins. The database is mainly used to search for fragments of protein backbone that are of interest, either because of their shape, or because of their relationship to other substructures (helices, sheets, loops). It also has a completely general query language (Daplex) which is founded on set-abstraction, list comprehensions and functions. It can call out to functions which may do arbitrary computations, combined with database search and updates. Most of the database system is written in compiled Prolog; this calls to C routines which access UNIX file structures. The Daplex language is compiled into Prolog and one can also write complex searches directly in Prolog.<
>